Geometry Nodes - How to procedurally subtract the unwanted part of a mesh after applying it with particles?
There are two ways to do that: 1) With Geometry Nodes (GN) itself or 2) with Geometry Nodes (GN) and Shader Nodes (SH).
Method 1:
First distribute the ponits/particles then generate volume mesh from those points. Next, boolean the input mesh mesh with volume mesh and combine it with the points/particles mesh.

Blend File:


Method 2:
In this case, we generate a Vertex Color based on the distance to the points/particles then use this as mask in the Shader Nodes to make that area of mesh transparent,

Blend File: